1 Search Results for "Muggli, Martin D."

A Succinct Solution to Rmap Alignment

Authors: Martin D. Muggli, Simon J. Puglisi, and Christina Boucher

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

We present Kohdista, which is an index-based algorithm for finding pairwise alignments between single molecule maps (Rmaps). The novelty of our approach is the formulation of the alignment problem as automaton path matching, and the application of modern index-based data structures. In particular, we combine the use of the Generalized Compressed Suffix Array (GCSA) index with the wavelet tree in order to build Kohdista. We validate Kohdista on simulated E. coli data, showing the approach successfully finds alignments between Rmaps simulated from overlapping genomic regions. Lastly, we demonstrate Kohdista is the only method that is capable of finding a significant number of high quality pairwise Rmap alignments for large eukaryote organisms in reasonable time. Kohdista is available at https://github.com/mmuggli/KOHDISTA/.

Cite as

Martin D. Muggli, Simon J. Puglisi, and Christina Boucher. A Succinct Solution to Rmap Alignment. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 12:1-12:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

  author =	{Muggli, Martin D. and Puglisi, Simon J. and Boucher, Christina},
  title =	{{A Succinct Solution to Rmap Alignment}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.12},
  URN =		{urn:nbn:de:0030-drops-93143},
  doi =		{10.4230/LIPIcs.WABI.2018.12},
  annote =	{Keywords: Optical mapping, index based data structures, FM-index, graph algorithms}
  • Refine by Author
  • 1 Boucher, Christina
  • 1 Muggli, Martin D.
  • 1 Puglisi, Simon J.

  • Refine by Classification
  • 1 Applied computing → Bioinformatics

  • Refine by Keyword
  • 1 FM-index
  • 1 Optical mapping
  • 1 graph algorithms
  • 1 index based data structures

  • Refine by Type
  • 1 document

  • Refine by Publication Year
  • 1 2018

Questions / Remarks / Feedback

Feedback for Dagstuhl Publishing

Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail